Abstract
Recombination leads to the generation of new viral progeny which remain undetected by routine testing procedures and may be a threat to the infected host. Here, we have characterised the complete genome sequences of two isolates of Apple stem pitting virus from apple cv. Red Chief (Palampur) and cv. Gold Spur (N) with distinct serological reactivities. The viral genomes consisted of 9267 nucleotides for isolate Palampur and 9254 nucleotides for isolate N, excluding the poly (A) tail and contained 5five open reading frames (ORFs). Isolate N shared 80.8% sequence identity with ASPV apple isolate GA2 from China, while isolate Palampur shared 81.4% sequence identity with ASPV apple isolate PB66 from the United Kingdom. The serological difference of isolates N and Palampur along with their low sequence identity indicated the existence of two distinct virus genotypes which was corroborated by evolutionary and genetic differentiation analyses. Recombination events were detected in the RdRp and CP sequences of Palampur isolate thereby suggesting the role of recombination in the evolution of distinct virus genotypes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02798-5.